Yogi, the PiCapture boards are constrained to deliver video to the GPU at the same resolution as the Raspberry Pi camera. For “Mode 6” 640×480 the video is resampled horizontally and cropped vertically. Unfortunately, there is no other solution that avoids cropping.
Many sources allow selection of PAL or NTSC formats. If this is the case for your source you might try NTSC – the is less cropping required for that format.